Edit: It's apparently not a duplication issue at all. The blocks for those entries are incorrect. Sometimes using ; instead of : and having a trailing : when it isnt needed. I'm not sure what is wrong with JCThaumcraft/shardstones and JCRailcraft/dirt though?

Ok, working versions of the railcraft and thaumcraft generators are below. I lowered the numClusters to 3 and I'd suggest lowering them further, possibly even make it every 5-10 chunks as well. As it was, a single ravine would give you more thaumcraft shards than you would ever be able to use :)

Ok, working versions of the railcraft and thaumcraft generators are below. I lowered the numClusters to 3 and I'd suggest lowering them further, possibly even make it every 5-10 chunks as well. As it was, a single ravine would give you more thaumcraft shards than you would ever be able to use :)